Cysteine proteases (CPs) are involved in a myriad of actions that include not only protein degradation, but also play an essential biological role in infectious and systemic diseases such as cancer. CPs also act as biomarkers and can be reached by active-based probes for diagnostic and mechanistic purposes that are critical in health and disease. In this paper, we present the modulation of a CP panel of parasites and mammals (Trypanosoma cruzi cruzain, LmCPB, CatK, CatL and CatS), whose inhibition by nitrile peptidomimetics allowed the identification of specificity and selectivity for a given CP. The activity cliffs identified at the CP inhibition level are useful for retrieving trends through multiple structure–activity relationships. For two of the cruzain inhibitors (10g and 4e), both enthalpy and entropy are favourable to Gibbs binding energy, thus overcoming enthalpy–entropy compensation (EEC). Group contribution of individual molecular modification through changes in enthalpy and entropy results in a separate partition on the relative differences of Gibbs binding energy (ΔΔG). Overall, this study highlights the role of CPs in polypharmacology and multi-target screening, which represents an imperative trend in the actual drug discovery effort.

半胱氨酸蛋白酶（CPs）参与多种动作，这些动作不仅包括蛋白质降解，而且在诸如癌症的传染性和系统性疾病中起着至关重要的生物学作用。CP也可作为生物标记物，并且可以通过基于活性的探针来达到，以用于对健康和疾病至关重要的诊断和机械用途。在本文中，我们介绍了对寄生虫和哺乳动物（锥虫锥虫，LmCPB，CatK，CatL和CatS）CP面板的调制，其受腈肽模拟物的抑制作用可确定给定CP的特异性和选择性。在CP抑制水平确定的活动悬崖对于通过多种结构-活动关系检索趋势很有用。对于两种Cruzain抑制剂（10g和4e），焓和熵都有利于吉布斯结合能，因此克服了焓-熵补偿（EEC）。通过焓和熵的变化，单个分子修饰的基团贡献导致吉布斯结合能的相对差异（ΔΔG）的单独分配。总的来说，这项研究强调了CPs在多药理学和多目标筛选中的作用，这代表了实际药物发现工作中的必然趋势。